DOCSLIB.ORG

Supplementary Material

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Material CSIRO PUBLISHING www.publish.csiro.au/journals/fpb Functional Plant Biology 33, 1–24 Supplementary material: FP05139_AC Supplementary material Molecular targets of elevated [CO2] in leaves and stems of Populus deltoides: implications for future tree growth and carbon sequestration Nathalie DruartA,B, Marisa Rodríguez-BueyA, Greg Barron-GaffordC, Andreas SjödinA, Rishikesh BhaleraoB and Vaughan HurryA,D AUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umeå, Sweden. BUmeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 83 Umeå, Sweden. CBiosphere 2 Laboratory, Columbia University, Oracle AZ 85623 USA. Current address: Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85719, USA. DCorresponding author. Email: [email protected] Appendix S1 1.0 1.0 A B 0.5 0.5 0.0 0.0 –0.5 –0.5 –1.0 –1.0 Relative gene expression (log gene expression Relative ) 1.0 1.0 2 C D 0.5 0.5 0.0 0.0 –0.5 –0.5 2 ) Relative gene expression (log gene expression Relative –1.0 –1.0 1.0 1.0 E F 0.5 0.5 0.0 0.0 –0.5 –0.5 –1.0 –1.0 400 800 1200 400 800 1200 Ambient [CO2] (µmol mol–1) Validation of reproducibility of the hybridisations by comparing the hybridisation results of three genes for which two independent cDNA clones had been spotted on the array. (A, C, E leaves; B, D, F stems). (A, B) Protein phosphatase 2A, 65 kDa subunit. (C, D) Elicitor-inducible cytochrome P450. (E, F) Major storage protein. © CSIRO 2006 10.1071/FP05139_AC 1445-4408/0602001 2 Functional Plant Biology Supplementary material Appendix S2. [CO2]-responsive genes in leaves sorted according to functional categories, selected up-regulated clones under 800 or –1 1200 µmol mol [CO2] Values are fold-change and those printed in bold are statistically significant with B-statistic Ն10 Function Clone ID At gene ID 800/400 1200/400 1200/800 Metabolism (01) Cytochrome P-450 PU03116 At1g13710 4.34 2.29 7.60 Cytochrome P-450 PU03121 At1g13710 4.18 2.44 8.67 Cytochrome P-450 (CYP78A9) PU05505 At3g61880 1.34 2.19 1.60 Dihydroflavonol 4-reductase PU12089 At1g61720 4.80 2.22 2.15 Naringenin 3-dioxygenase PU01480 At3g51240 –1.01 1.70 1.71 Chalcone synthase PU10149 At5g13930 1.34 1.67 1.23 Chalcone synthase PU12625 At5g13930 1.18 1.49 1.25 Chalcone synthase 1 PU04294 At5g13930 2.07 1.49 1.25 Chalcone isomerase PU04986 At3g55120 1.23 1.45 1.28 Elicitor-inducible cytochrome P450 PU08702 At1g01280 4.49 4.26 3.12 Elicitor-inducible cytochrome P450 PU12599 At5g07990 8.84 4.74 2.57 Elicitor-inducible cytochrome P450 PU12470 At5g07990 1.80 4.43 2.50 Glucosyltransferase NTGT3 PU12170 At1g07250 1.39 2.04 1.46 IPP transferase-like protein PU04004 At5g20040 –1.17 1.83 2.14 Major storage protein PU03068 At4g24340 –9.1 2.05 2.18 Major storage protein PU03117 At4g24340 –1.11 2.34 2.53 Major storage protein PU03474 At4g24340 –1.22 2.09 2.28 Major storage protein PU03508 At4g24340 –5.86 2.48 2.58 Major storage protein PU03510 At4g24340 –2.23 2.51 2.51 Major storage protein PU03513 At4g24340 –1.77 2.42 2.73 Major storage protein PU03548 At4g24340 –1.07 2.44 2.63 Major storage protein PU03698 At4g24340 –7.79 2.50 2.64 Major storage protein PU03708 At4g24340 –1.17 2.35 2.55 Major storage protein PU03743 At4g24340 –1.56 2.36 2.63 Major storage protein PU03784 At4g24340 –7.19 2.49 2.62 Major storage protein PU03820 At4g24340 –7.61 2.36 2.49 Major storage protein PU03824 At4g24340 –4.04 2.34 2.41 Major storage protein PU04029 At4g24340 –8.11 2.35 2.48 Thioredoxin H PU01940 At1g59730 1.87 1.89 1.01 Xyloglucan endotransglycosylase PU02379 At4g03210 –1.49 2.09 2.32 Xyloglucan endotransglycosylase PU07373 At4g03210 2.11 2.40 2.07 Endo-xyloglucan transferase PU11514 At5g65730 1.17 2.00 1.70 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase PU02218 At1g22410 1.06 2.21 2.28 precursor Cell growth, cell division, DNA synthesis (03) Microtubule-associated protein EB1-like protein PU03283 At5g62500 –1.08 2.52 2.72 Protein phosphatase 2A 65 kDa regulatory subunit PU05097 At3g25800 1.18 2.65 2.23 Protein phosphatase 2A 65 kDa regulatory subunit PU12228 At3g25800 1.55 3.75 2.39 Protein phosphatase 2A 65 kDa regulatory subunit PU12736 At3g25800 1.59 4.11 2.56 RGA1, giberellin response modulation protein PU03640 At2g01570 –1.11 2.20 2.44 RING zinc finger ankyrin protein-related PU03201 At2g28840 –1.12 1.85 2.08 Transcription (04) CCAAT-binding factor B subunit PU03099 At1g72830 –1.09 2.12 2.30 Probable coproporphyrinogen oxidase PU03696 At3g20740 –1.09 2.30 2.51 Protein destination (06) Peptidylprolyl isomerase PU11811 At5g48570 1.24 3.68 2.94 Ubiquitin fusion-degradation protein PU03741 At2g21270 –1.04 2.24 2.32 18.5 kDa class I heat shock protein (HSP 18.5) PU04831 At5g59720 1.28 3.77 2.93 Cell rescue, defense, cell death and ageing (11) Disease resistance response protein-related PU03542 At1g58170 –1.10 2.01 2.20 Cellular organisation (30) Pollen allergen PU06328 At4g38400 1.91 –1.21 2.32 Supplementary material Functional Plant Biology 3 Appendix S2 continued Function Clone ID At gene ID 800/400 1200/400 1200/800 Classification not yet clear-cut (98) Expressed protein PU08410 At1g49750 1.93 1.60 –1.19 Expressed protein PU03138 At3g08780 –1.11 2.11 2.33 Expressed protein PU03140 At1g71430 –1.03 2.33 2.39 Expressed protein PU03233 At1g71080 –1.09 2.46 2.69 Expressed protein PU03245 At5g19260 –1.15 2.16 2.47 Expressed protein PU03333 At4g22920 1.05 2.29 2.17 Expressed protein PU03435 At4g01650 –1.12 2.02 2.26 Expressed protein PU03543 At4g39140 –1.07 2.13 2.28 Expressed protein PU03670 At2g21180 1.06 2.10 1.96 Expressed protein PU05874 At3g24100 1.12 2.10 1.87 Expressed protein PU06017 At4g24220 1.35 2.28 1.68 Expressed protein PU11113 At5g41080 –1.09 2.15 2.01 Expressed protein PU13336 At1g61720 2.09 2.93 2.54 Expressed protein PU07779 At5g11090 –1.31 1.76 2.32 Expressed protein PU11064 At5g41080 –7.97 2.01 Unknown protein PU03835 At1g71010 –1.07 2.09 2.22 Unclassified proteins (99) Boiling stable protein A PU00350 At3g17210 8.76 3.66 3.45 Boiling stable protein A PU01134 At3g17210 8.76 3.78 3.56 Cellulase, putative PU03243 At3g26130 –1.02 2.42 2.47 Cytochrome c oxidase polypeptide VIII PU09960 At5g23100 1.15 1.99 1.73 Expressed protein PU03457 At1g69050 –1.09 2.44 2.65 Expressed protein PU03578 At1g22420 –1.10 2.51 2.77 Expressed protein PU11117 At4g29200 1.50 –1.70 1.99 GDSL-motif lipase/hydrolase-like protein PU10319 At5g45670 2.65 1.99 9.64 GDSL-motif lipase/hydrolase-like protein PU12148 At5g45670 1.27 2.42 2.21 GDSL-motif lipase/hydrolase-like protein PU12188 At5g45670 9.55 2.49 2.33 GDSL-motif lipase/hydrolase-like protein PU12468 At5g45670 2.96 2.64 2.15 HEN1 PU12175 At4g20910 –1.06 2.18 2.30 Major storage protein PU03509 At3g17650 –1.09 2.34 2.57 Possibly polygalacturonase inhibiting protein PU08796 At5g06870 4.93 –1.20 –5.94 Polyphenol oxidase PU12604 At1g08170 3.92 2.73 –1.44 Protease inhibitor II PU03669 At2g02130 2.57 2.57 2.88 ORFs (Putative primordial protein) PU11210 At5g40260 –1.50 1.36 2.05 4 Functional Plant Biology Supplementary material Appendix S3. [CO2]-responsive genes in leaves sorted according to functional categories, selected down-regulated clones under –1 800 or 1200 µmol mol [CO2] Values are fold-change and those printed in bold are statistically significant with B-statistic Ն10 Function Clone ID At gene ID 800/400 1200/400 1200/800 Metabolism (01) GDP-mannose pyrophosphorylase PU07331 At2g39770 –4.58 –1.79 2.55 Inositol-3-phosphate synthase PU13206 At5g10170 1.50 –1.31 –1.98 Transcription (04) DNA-binding protein, putative PU10896 At1g01060 5.90 –4.68 –2.18 DNA-binding protein, putative PU13388 At1g01060 7.60 –5.66 –2.51 Protein destination (06) DnaJ-like protein PU10218 At2g17880 –2.02 –8.67 1.46 DnaJ-like protein PU12884 At2g17880 –1.99 –7.49 2.46 DnaJ-like protein PU13066 At2g17880 –1.93 –8.53 9.26 Cell fate (14) Floricaula/leafy homolog (PTLF) PU00007 At5g61850 1.25 –2.50 –2.63 Floricaula/leafy homolog (PTLF) PU00843 At5g61850 7.42 –2.39 –2.52 Floricaula/leafy homolog (PTLF) PU03491 At5g61850 1.76 –2.14 –2.42 Floricaula/leafy homolog (PTLF) PU03680 At5g61850 1.95 –2.33 –2.37 Floricaula/leafy homolog (PTLF) PU03755 At5g61850 1.21 –2.38 –2.40 Floricaula/leafy homolog (PTLF) PU05650 At5g61850 3.41 –2.20 –2.26 Floricaula/leafy homolog (PTLF) PU12065 At5g61850 1.18 –2.62 –2.85 Floricaula/leafy homolog (PTLF) PU12438 At5g61850 3.78 –2.43 –2.50 Floricaula/leafy homolog (PTLF) PU13110 At5g61850 1.69 –2.35 –2.64 Cellular communication/signal transduction (10) Protein kinase PU13475 At2g30360 1.27 –1.54 –1.96 Cellular organisation (30) GAB3. Possibly expansin-like protein PU09319 At1g69530 –1.51 –2.06 –1.36 Classification not yet clear-cut (98) Expressed protein PU01650 At1g26800 1.26 –1.68 –2.12 Expressed protein PU08923 At1g10560 1.09 –1.97 –1.80 Unclassified proteins (99) Possibly polygalacturonase inhibiting protein PU08796 At5g06870 4.93–1.20 –5.94 Ribonucleoside-diphosphate reductase α-chain PU09892 At1g10330 –1.09 –1.80 –2.02 Supplementary material Functional Plant Biology 5 Appendix S4.
Load more

Recommended publications
  • Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: a Review
    molecules Review Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: A Review Hanghang Lou 1,†, Lifei Hu 2,†, Hongyun Lu 1, Tianyu Wei 1 and Qihe Chen 1,* 1 Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; [email protected] (H.L.); [email protected] (H.L.); [email protected] (T.W.) 2 Hubei Key Lab of Quality and Safety of Traditional Chinese Medicine & Health Food, Huangshi 435100, China; [email protected] * Correspondence: [email protected]; Tel.: +86-0571-8698-4316 † These authors are equally to this manuscript. Abstract: Flavonoids belong to a class of plant secondary metabolites that have a polyphenol structure. Flavonoids show extensive biological activity, such as antioxidative, anti-inflammatory, anti-mutagenic, anti-cancer, and antibacterial properties, so they are widely used in the food, phar- maceutical, and nutraceutical industries. However, traditional sources of flavonoids are no longer sufficient to meet current demands. In recent years, with the clarification of the biosynthetic pathway of flavonoids and the development of synthetic biology, it has become possible to use synthetic metabolic engineering methods with microorganisms as hosts to produce flavonoids. This article mainly reviews the biosynthetic pathways of flavonoids and the development of microbial expression systems for the production of flavonoids in order to provide a useful reference for further research on synthetic metabolic engineering of flavonoids. Meanwhile, the application of co-culture systems in the biosynthesis of flavonoids is emphasized in this review. Citation: Lou, H.; Hu, L.; Lu, H.; Wei, Keywords: flavonoids; metabolic engineering; co-culture system; biosynthesis; microbial cell factories T.; Chen, Q.
    [Show full text]
  • Key Enzymes Involved in the Synthesis of Hops Phytochemical Compounds: from Structure, Functions to Applications
    International Journal of Molecular Sciences Review Key Enzymes Involved in the Synthesis of Hops Phytochemical Compounds: From Structure, Functions to Applications Kai Hong , Limin Wang, Agbaka Johnpaul , Chenyan Lv * and Changwei Ma * College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qinghua Donglu Road, Haidian District, Beijing 100083, China; [email protected] (K.H.); [email protected] (L.W.); [email protected] (A.J.) * Correspondence: [email protected] (C.L.); [email protected] (C.M.); Tel./Fax: +86-10-62737643 (C.M.) Abstract: Humulus lupulus L. is an essential source of aroma compounds, hop bitter acids, and xanthohumol derivatives mainly exploited as flavourings in beer brewing and with demonstrated potential for the treatment of certain diseases. To acquire a comprehensive understanding of the biosynthesis of these compounds, the primary enzymes involved in the three major pathways of hops’ phytochemical composition are herein critically summarized. Hops’ phytochemical components impart bitterness, aroma, and antioxidant activity to beers. The biosynthesis pathways have been extensively studied and enzymes play essential roles in the processes. Here, we introduced the enzymes involved in the biosynthesis of hop bitter acids, monoterpenes and xanthohumol deriva- tives, including the branched-chain aminotransferase (BCAT), branched-chain keto-acid dehydroge- nase (BCKDH), carboxyl CoA ligase (CCL), valerophenone synthase (VPS), prenyltransferase (PT), 1-deoxyxylulose-5-phosphate synthase (DXS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), Geranyl diphosphate synthase (GPPS), monoterpene synthase enzymes (MTS), cinnamate Citation: Hong, K.; Wang, L.; 4-hydroxylase (C4H), chalcone synthase (CHS_H1), chalcone isomerase (CHI)-like proteins (CHIL), Johnpaul, A.; Lv, C.; Ma, C.
    [Show full text]
  • Building Blue E. Coli: Engineering the Anthocyanin Biosynthetic Pathway
    Building blue E. coli: Engineering the anthocyanin biosynthetic pathway Leah Johnston1, Lucas Jarche1, Alexander Porter1, Julie Ryu1, Emma Price1, Emma Finlayson-Trick1, Khaled Aly1, Paul Bissonnette2, Eric Pace3, Dr. John Rohde1 1Department of Microbiology and Immunology, 2Department of Chemistry, 3Department of Agriculture Dalhousie University, Halifax, Canada, B3H 1X5 THE ANTHOCYANIN PATHWAY METHODS RESULTS 1kb (B) Method of Template DNA for each of the genes required for the production of the Anthocyanin biosynthetic Gene Size (bp) Function Epitope ladder (B) Acquisition of pathway in E. coli were acquired from the following sources outlined in Figure 1 (B). (A) Name Tag Template DNA 10 Phenylalanine Lyase involved in Amplified from A. (A) 2762 polyphenol S-Tag thaliana cDNA, Ammonia . synthesis. insert in Phenylalanine Ammonia Lyase and 4-Coumaroyl CoA Ligase were acquired as inserts in a 3.0. Lyase pACYCDuet-1 pACYCDuet-1 plasmid from Sinyuan Wang et. al (2005) at Utah State University. Cinnamate 4- 2.0 Phenylalanine from Utah State Hydroxylase-HA fusion protein was inserted into this plasmid at the end of the PAL coding region 1.5 Phenylalanine ammonia lyase University using restriction enzymes and transformed into BL21 CaCl2 competent E. coli with T7 RNA Cinnamate 4- Oxidoreductase Amplified from A. Cinnamic Acid 1518 involved in HA-Tag thaliana cDNA, Polymerase activity. A western blot with anti-HA antibody was used to detect the presence of the 1.0 Hydroxylase phenylalanine purchased from C4H fusion protein in the resultant cells. Cinnamate 4-hydroxylase metabolism. TAIR database P-Coumaric Acid 4-Coumaroyl Ligase involved in Insert in 2546 phenylpropanoid His-Tag pACYCDuet-1 Chalcone Synthase, Chalcone Isomerase and Flavanone 3-Hydroxylase were amplified from the CoA Ligase 0.5 4-coumaryl-coenzyme A ligase biosynthesis.
    [Show full text]
  • Analysis of the Chromosomal Clustering of Fusarium-Responsive
    www.nature.com/scientificreports OPEN Analysis of the chromosomal clustering of Fusarium‑responsive wheat genes uncovers new players in the defence against head blight disease Alexandre Perochon1,2, Harriet R. Benbow1,2, Katarzyna Ślęczka‑Brady1, Keshav B. Malla1 & Fiona M. Doohan1* There is increasing evidence that some functionally related, co‑expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium‑responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non‑metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin‑like proteins. 20 of the FRGCs encode nonhomologous, non‑metabolic genes (including defence‑related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium‑ responsive genes, fve of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specifc traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease. Prokaryote genomes encode co-transcribed genes with related functions that cluster together within operons. Clusters of functionally related genes also exist in eukaryote genomes, including fungi, nematodes, mammals and plants1.
    [Show full text]
  • Transcription Factors Regulating Terpene Synthases in Tomato Trichomes
    UvA-DARE (Digital Academic Repository) Transcription factors regulating terpene synthases in tomato trichomes Spyropoulou, E. Publication date 2012 Document Version Final published version Link to publication Citation for published version (APA): Spyropoulou, E. (2012). Transcription factors regulating terpene synthases in tomato trichomes. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:03 Oct 2021 Transcription factors regulating terpene synthases in tomato trichomes factors regulating Transcription Transcription factors regulating terpene synthases in tomato trichomes Eleni Spyropoulou Eleni Spyropoulou Transcription factors regulating terpene synthases in tomato trichomes ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam op gezag van de Rector Magnificus prof. dr. D.C. van den Boom ten overstaan van een door het college voor promoties ingestelde commissie, in het openbaar te verdedigen in de Agnietenkapel op dinsdag 03 juli 2012, te 16:00 uur door Eleni Spyropoulou geboren te Marousi, Griekenland PROMOTIECOMISSIE Promotor Prof.
    [Show full text]
  • Noncatalytic Chalcone Isomerase-Fold Proteins in Humulus Lupulus Are Auxiliary Components in Prenylated Flavonoid Biosynthesis
    Noncatalytic chalcone isomerase-fold proteins in Humulus lupulus are auxiliary components in prenylated flavonoid biosynthesis Zhaonan Bana,b, Hao Qina, Andrew J. Mitchellc, Baoxiu Liua, Fengxia Zhanga, Jing-Ke Wengc,d, Richard A. Dixone,f,1, and Guodong Wanga,1 aState Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; bUniversity of Chinese Academy of Sciences, 100049 Beijing, China; cWhitehead Institute for Biomedical Research, Cambridge, MA 02142; dDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; eBioDiscovery Institute, University of North Texas, Denton, TX 76203; and fDepartment of Biological Sciences, University of North Texas, Denton, TX 76203 Contributed by Richard A. Dixon, April 25, 2018 (sent for review February 6, 2018; reviewed by Joerg Bohlmann and Mattheos A. G. Koffas) Xanthohumol (XN) and demethylxanthohumol (DMX) are special- braries have been deposited in the TrichOME database [www. ized prenylated chalconoids with multiple pharmaceutical appli- planttrichome.org (18)], and numerous large RNAseq datasets from cations that accumulate to high levels in the glandular trichomes different hop tissues or cultivars have also been made publically of hops (Humulus lupulus L.). Although all structural enzymes in available. By mining the hops transcriptome data, we and others have the XN pathway have been functionally identified, biochemical functionally identified several key terpenophenolic biosynthetic en- mechanisms underlying highly efficient production of XN have zymes from hop glandular trichomes (1, 18–23); these include car- not been fully resolved. In this study, we characterized two non- boxyl CoA ligase (CCL) genes and two aromatic prenyltransferase catalytic chalcone isomerase (CHI)-like proteins (designated as (PT) genes (HlPT1L and HlPT2) (22, 23).
    [Show full text]
  • De Novo Sequencing and Comparative Analysis of Holy and Sweet Basil
    Rastogi et al. BMC Genomics 2014, 15:588 http://www.biomedcentral.com/1471-2164/15/588 RESEARCH ARTICLE Open Access De novo sequencing and comparative analysis of holy and sweet basil transcriptomes Shubhra Rastogi1, Seema Meena1, Ankita Bhattacharya1, Sumit Ghosh1, Rakesh Kumar Shukla1, Neelam Singh Sangwan2, Raj Kishori Lal3, Madan Mohan Gupta4, Umesh Chandra Lavania3, Vikrant Gupta1, Dinesh A Nagegowda1* and Ajit Kumar Shasany1* Abstract Background: Ocimum L. of family Lamiaceae is a well known genus for its ethnobotanical, medicinal and aromatic properties, which are attributed to innumerable phenylpropanoid and terpenoid compounds produced by the plant. To enrich genomic resources for understanding various pathways, de novo transcriptome sequencing of two important species, O. sanctum and O. basilicum, was carried out by Illumina paired-end sequencing. Results: The sequence assembly resulted in 69117 and 130043 transcripts with an average length of 1646 ± 1210.1 bp and 1363 ± 1139.3 bp for O. sanctum and O. basilicum, respectively. Out of the total transcripts, 59648 (86.30%) and 105470 (81.10%) from O. sanctum and O. basilicum, and respectively were annotated by uniprot blastx against Arabidopsis, rice and lamiaceae. KEGG analysis identified 501 and 952 transcripts from O. sanctum and O. basilicum, respectively, related to secondary metabolism with higher percentage of transcripts for biosynthesis of terpenoids in O. sanctum and phenylpropanoids in O. basilicum. Higher digital gene expression in O. basilicum was validated through qPCR and correlated to higher essential oil content and chromosome number (O. sanctum, 2n = 16; and O. basilicum, 2n = 48). Several CYP450 (26) and TF (40) families were identified having probable roles in primary and secondary metabolism.
    [Show full text]
  • Comprehensive Metabolic and Transcriptomic Profiling of Various
    www.nature.com/scientificreports OPEN Comprehensive metabolic and transcriptomic profling of various tissues provide insights for saponin Received: 17 October 2017 Accepted: 4 June 2018 biosynthesis in the medicinally Published: xx xx xxxx important Asparagus racemosus Prabhakar Lal Srivastava1, Anurag Shukla2 & Raviraj M. Kalunke2 Asparagus racemosus (Shatavari), belongs to the family Asparagaceae and is known as a “curer of hundred diseases” since ancient time. This plant has been exploited as a food supplement to enhance immune system and regarded as a highly valued medicinal plant in Ayurvedic medicine system for the treatment of various ailments such as gastric ulcers, dyspepsia, cardiovascular diseases, neurodegenerative diseases, cancer, as a galactogogue and against several other diseases. In depth metabolic fngerprinting of various parts of the plant led to the identifcation of 13 monoterpenoids exclusively present in roots. LC-MS profling led to the identifcation of a signifcant number of steroidal saponins (33). However, we have also identifed 16 triterpene saponins for the frst time in A. racemosus. In order to understand the molecular basis of biosynthesis of major components, transcriptome sequencing from three diferent tissues (root, leaf and fruit) was carried out. Functional annotation of A. racemosus transcriptome resulted in the identifcation of 153 transcripts involved in steroidal saponin biosynthesis, 45 transcripts in triterpene saponin biosynthesis, 44 transcripts in monoterpenoid biosynthesis and 79 transcripts in favonoid biosynthesis. These fndings will pave the way for better understanding of the molecular basis of steroidal saponin, triterpene saponin, monoterpenoids and favonoid biosynthesis in A. racemosus. Asparagus racemosus is one of the most valuable medicinal plants, regarded as a “Queen of herbs” in Ayurvedic health system and has been used worldwide to cure various diseases1.
    [Show full text]
  • (Ophiopogon Japonicus (Lf) Ker-Gawl
    www.nature.com/scientificreports OPEN De novo assembly and annotation of the Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) Received: 23 December 2016 Accepted: 5 May 2017 transcriptome in different growth Published: xx xx xxxx stages Huijun Liu1, Ying Wang2,3, Tingzhang Wang2,3, Xuhui Ying6, Rongrong Wu4,5 & Huan Chen1,2,3 Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) is a traditional medicinal herb in the family Liliaceae that has significant pharmacological effects on immunity and cardiovascular disease. In this study, three different growth stages of Zhe-Maidong were investigated using RNA-seq, and a total of 16.4 Gb of raw data was obtained. After filtering and assembling, 96,738 unigenes with an average length of 605.3 bp were ultimately generated. A total of 77,300 unigenes were annotated using information from five databases, including the NT, NR, SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. Additionally, the mechanisms of flavonoid, saponin and polysaccharide biosynthesis and of accumulation at different stages of tuber development were also characterized. From the first to third years, the contents of flavonoids, saponins and polysaccharides all increased, whereas the expression levels of related genes decreased in the flavonoid and saponin pathways and first increased and then decreased in the polysaccharide pathway. The results of this study provide the most comprehensive expressed sequence resource for Zhe-Maidong and will expand the available O. japonicus gene library and facilitate further genome-wide research and analyses of this species. Zhe-Maidong (ZMD), also known as Ophiopogon japonicus (L.f.) Ker-Gawl, is an evergreen perennial in the Liliaceae family and a famous Chinese traditional medicinal herb.
    [Show full text]
  • Download PDF (1288K)
    Plant Biotechnology 31, 465–482 (2014) DOI: 10.5511/plantbiotechnology.14.1003a Review Microbial production of plant specialized metabolites Shiro Suzuki1,3,*, Takao Koeduka2, Akifumi Sugiyama1, Kazufumi Yazaki1, Toshiaki Umezawa1,3 1 Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan; 2 Faculty of Agriculture, Yamaguchi University, Yamaguchi 753-8515, Japan; 3 Institute of Sustainability Science, Kyoto University, Uji, Kyoto 611-0011, Japan * E-mail: [email protected] Tel: +81-774-38-3624 Fax: +81-774-38-3682 Received July 22, 2014; accepted October 3, 2014 (Edited by T. Shoji) Abstract Plant specialized metabolites play important roles in human life. These metabolites, however, are often produced in small amounts in particular plant species. Moreover, some of these species are endangered in their natural habitats, thus further limiting the availability of some plant specialized metabolites. Microbial production of these compounds may circumvent this problem. Considerable progress has been made in the microbial production of various plant specialized metabolites over the past decade. Now, the microbial production of these compounds is becoming robust, fine-tuned, and commercially relevant systems using the methods of synthetic biology. This review describes the progress of microbial production of plant specialized metabolites, including phenylpropanoids, flavonoids, stilbenoids, diarylheptanoids, phenylbutanoids, terpenoids, and alkaloids, and discusses future challenges in this field.
    [Show full text]
  • 12) United States Patent (10
    US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.
    [Show full text]
  • Characterization of Natural Product Biological Imprints for Computer-Aided Drug Design Applications Noe Sturm
    Characterization of natural product biological imprints for computer-aided drug design applications Noe Sturm To cite this version: Noe Sturm. Characterization of natural product biological imprints for computer-aided drug design applications. Cheminformatics. Université de Strasbourg, 2015. English. NNT : 2015STRAF059. tel-01300872 HAL Id: tel-01300872 https://tel.archives-ouvertes.fr/tel-01300872 Submitted on 11 Apr 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES CHIMIQUES Laboratoire d’Innovation Thérapeutique, UMR 7200 en cotutelle avec Eskitis Institute for Drug Discovery, Griffith University THÈSE présentée par Noé STURM soutenue le : 8 Décembre 2015 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline/Spécialité : Chimie/Chémoinformatique Caractérisation de l’empreinte biologique des produits naturels pour des applications de conception rationnelle de médicament assistée par ordinateur THÈSE dirigée par : KELLENBERGER Esther Professeur, Université de Strasbourg QUINN Ronald Professeur, Université de Griffith, Brisbane, Australie RAPPORTEURS : IORGA Bogdan Chargé de recherche HDR, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette GÜNTHER Stefan Professeur, Université Albert Ludwigs, Fribourg, Allemagne Acknowledgments First of all, I would like to thank my two supervisors Professor Kellenberger Esther and Professor Quinn Ronald for their excellent assistance, both academic and personal in nature.
    [Show full text]